a little bit confused #22

hamazaki1990/individual.py

@@ -2,11 +2,12 @@
 
 
 class Individual:
-    def __init__(self, n, f=1.0, mutationrate=0.0):
+    mutationrate = 0.01
+
+    def __init__(self, n, f=1.0):
         self._id = n
         self._fitness = f
         self._genotype = []
-        self._mutationrate = mutationrate
 
     def get_id(self):
         return self._id
@@ -20,7 +21,7 @@ def get_genotype(self):
     def acquire_mutation(self):
         r = random.random()
         next_genotype = self._genotype
-        if r < self._mutationrate:
+        if r < Individual.mutationrate:
             next_genotype.append(random.random())
         self._genotype = next_genotype
 
@@ -33,7 +34,7 @@ def main():
     print(ind.get_id())
     print(ind.get_fitness())
 
-    ind2 = Individual(30, 0.8, 1.0)
+    ind2 = Individual(30, 0.8)
     print(ind2.get_id())
     print(ind2.get_fitness())
     ind2.acquire_mutation()
@@ -43,8 +44,8 @@ def main():
     print(ind2.get_id())
     print(ind2.get_fitness())
 
-    ind3 = Individual(0, 1.0, 0.8)
-    ind4 = Individual(1, 1.0, 0.8)
+    ind3 = Individual(0, 1.0)
+    ind4 = Individual(1, 1.0)
     pop = [ind3, ind4]
     print([x.get_genotype() for x in pop])
     [x.acquire_mutation() for x in pop]

hamazaki1990/population.py

@@ -10,10 +10,10 @@ def roulettechoice(individuals, cumsum_fitness):
 
 
 class Population:
-    def __init__(self, n, mutant=0, s=0, mutationrate=0.0):
+    def __init__(self, n, mutant=0, s=0):
         num_mutant = int(n * mutant)
-        mutant_inds = [Individual(x, 1 + s, mutationrate) for x in range(num_mutant)]
-        wild_inds = [Individual(x, 1, mutationrate) for x in range(num_mutant, n)]
+        mutant_inds = [Individual(x, 1 + s) for x in range(num_mutant)]
+        wild_inds = [Individual(x, 1) for x in range(num_mutant, n)]
         self._inds = mutant_inds + wild_inds
 
     def get_ids(self):
@@ -23,39 +23,38 @@ def get_fitnesses(self):
         fitness = [x.get_fitness() for x in self._inds]
         return fitness
 
-    def get_mutantfreq(self):
-        fitness = [x.get_fitness() for x in self._inds]
-        mutantfreq = 1 - fitness.count(1.0)/len(fitness)
-        return mutantfreq
+    def get_genotypes(self):
+        genotypes = [x.get_genotype() for x in self._inds]
+        return genotypes
 
     def next_genwf(self):
         fitness = [x.get_fitness() for x in self._inds]
         size = len(self._inds)
         cumsum_fitness = [sum(fitness[:i]) for i in range(1, size + 1)]
         next_generation = []
         for x in range(size):
-            next_generation.append(roulettechoice(self._inds, cumsum_fitness))
+            next_inds = roulettechoice(self._inds, cumsum_fitness)
+            next_inds.acquire_mutation()
+            next_generation.append(next_inds)
         self._inds = next_generation
 
     def next_genmo(self):
         fitness = [x.get_fitness() for x in self._inds]
         size = len(self._inds)
         cumsum_fitness = [sum(fitness[:i]) for i in range(1, size + 1)]
         i_dying = random.randrange(size)
-        self._inds[i_dying] = roulettechoice(self._inds, cumsum_fitness)
-
-    def acquire_mutations(self):
-        [x.acquire_mutation() for x in self._inds]
-        genotypes = [x.get_genotype() for x in self._inds]
-        return genotypes
+        next_inds = roulettechoice(self._inds, cumsum_fitness)
+        next_inds.acquire_mutation()
+        self._inds[i_dying] = next_inds
 
     def list_mutation(self):
         genotypes = [x.get_genotype() for x in self._inds]
         m_sites = []
         for x in genotypes:
             m_sites.extend(x)
         m_sites = sorted(m_sites)
-        m_list = [[0 for x in range(len(m_sites))] for y in range(len(self._inds))]
+        m_list = ([[0 for x in range(len(m_sites))]
+                  for y in range(len(self._inds))])
         for i in range(len(self._inds)):
             for j in range(len(genotypes[i])):
                 k = m_sites.index(genotypes[i][j])
@@ -70,67 +69,46 @@ def is_not_fixed(self):
         else:
             return False
 
-    def mutation_is_not_fixed(self):
-        fitness = [x.get_fitness() for x in self._inds]
-        for x in range(1, len(fitness)):
-            if fitness[0] != fitness[x]:
-                return True
-        else:
-            return False
-
 
 def main():
     p1_1 = Population(10)
     print(p1_1.get_ids())
     print(p1_1.get_fitnesses())
     print(p1_1.is_not_fixed())
-    print(p1_1.mutation_is_not_fixed())
 
-    for x in range(20):
+    for x in range(10):
         p1_1.next_genwf()
         print(p1_1.get_ids())
-        print(p1_1.get_fitnesses())
+        print(p1_1.get_genotypes())
+        p1_1.list_mutation()
+
     print(p1_1.is_not_fixed())
-    print(p1_1.mutation_is_not_fixed())
+    p1_1.list_mutation()
 
     p1_2 = Population(10, 0.3, 0.2)
     print(p1_2.get_ids())
     print(p1_2.get_fitnesses())
     print(p1_2.is_not_fixed())
-    print(p1_2.mutation_is_not_fixed())
-    print(p1_2.get_mutantfreq())
-
-    for x in range(20):
-        p1_2.next_genwf()
-        print(p1_2.get_ids())
-    print(p1_2.get_fitnesses())
-    print(p1_2.is_not_fixed())
-    print(p1_2.mutation_is_not_fixed())
 
     p2_1 = Population(10)
     print(p2_1.get_ids())
     print(p2_1.get_fitnesses())
 
-    for x in range(20):
+    for x in range(10):
         p2_1.next_genmo()
         print(p2_1.get_ids())
     print(p2_1.get_fitnesses())
+    p2_1.list_mutation()
 
     p2_2 = Population(10, 0.3, 0.2)
     print(p2_2.get_ids())
     print(p2_2.get_fitnesses())
 
-    for x in range(20):
+    for x in range(10):
         p2_2.next_genmo()
         print(p2_2.get_ids())
     print(p2_2.get_fitnesses())
-
-    p3_1 = Population(10, 0, 0, 0.8)
-    p3_1.list_mutation()
-    print(p3_1.acquire_mutations())
-    p3_1.list_mutation()
-    print(p3_1.acquire_mutations())
-    p3_1.list_mutation()
+    p2_2.list_mutation()
 
 
 if __name__ == '__main__':

hamazaki1990/visualize.py

@@ -2,23 +2,34 @@
 from population import Population
 
 
+def calculate_mutantfreq(population):
+    m_list = population.list_mutation()
+    m_count = [0 for x in range(len(m_list[0]))]
+    for i in m_list:
+        for j in m_list[i]:
+            if i[j] != 0:
+                m_count[j] += 1
+    mutantfreq = [x/len(m_list) for x in m_count]
+    return mutantfreq
+
+
 def change_allelewf(population):
     t = 0
-    fixprocess = [[t, population.get_mutantfreq()]]
-    while population.mutation_is_not_fixed():
+    fixprocess = [[t, population.calculate_mutantfreq()]]
+    for x in range(20):
         t += 1
         population.next_genwf()
-        fixprocess.append([t, population.get_mutantfreq()])
+        fixprocess.append([t, population.calculate_mutantfreq()])
     return fixprocess
 
 
 def change_allelemo(population):
     t = 0
-    fixprocess = [[t, population.get_mutantfreq()]]
-    while population.mutation_is_not_fixed():
+    fixprocess = [[t, population.calculate_mutantfreq()]]
+    for x in range(20):
         t += 1
         population.next_genmo()
-        fixprocess.append([t, population.get_mutantfreq()])
+        fixprocess.append([t, population.calculate_mutantfreq()])
     return fixprocess